Methods and compositions for identification of tumor models

Abstract

The disclosure provides methods and compositions, e.g., kits, for identifying or authenticating a sample, e.g., a tumor model, based on the genotype of the sample at a group of SNP loci.

What is claimed is: 
     
       1. A method for determining the authentication of a human or mouse sample, the method comprising:
 obtaining a nucleic acid from the human or mouse sample; 
 providing a set of oligonucleotide primer pairs, wherein each oligonucleotide primer pair in the set flanks a single locus in a set of single nucleotide polymorphism (SNP) loci of (i) SEQ ID NOs: 1-237 or (ii) SEQ ID NOs: 238-436, and wherein each oligonucleotide primer pair is capable of amplifying a single locus from the set of SNP loci in a multiplex amplification reaction; 
 co-amplifying the set of SNP loci in a multiplex amplification reaction, wherein the product of the multiplex amplification reaction comprises a mixture of amplified alleles from each of the co-amplified loci in the set of SNP loci; 
 evaluating the products of the co-amplification reaction to determine the alleles present at each of the set of SNP loci within the human or mouse sample; 
 comparing the alleles present at each of the set of SNP loci within the sample with alleles present at each of the set of SNP loci in a human or mouse reference sample; and 
 determining whether (i) the human or mouse sample is the same as the human or mouse reference sample, or (ii) the human or mouse sample contains a contaminant other than the human or mouse reference sample. 
 
     
     
       2. The method of  claim 1 , wherein the human or mouse sample is a cell, a tissue, an organoid, or a combination thereof. 
     
     
       3. The method of  claim 2 , wherein the human or mouse sample is a cell line or a tumor tissue. 
     
     
       4. The method of  claim 1 , wherein the human or mouse sample contains a contaminant, the method further comprising determining the percentage of the contaminant in the human or mouse sample. 
     
     
       5. The method of  claim 1 , wherein the human or mouse sample contains a contaminant, the method further comprising determining the identity of the contaminant. 
     
     
       6. The method of  claim 1 , wherein the products of the co-amplification reaction are evaluated by next-generation sequencing (NGS). 
     
     
       7. The method of  claim 1 , wherein the nucleic acid is barcoded. 
     
     
       8. The method of  claim 1 , further comprising identifying the gender of a subject from which the sample is obtained by analyzing at least one sex chromosome SNP locus. 
     
     
       9. The method of  claim 1 , wherein the human or mouse sample is a mouse sample from a mouse tumor model selected from the group consisting of 4T1, A20, B16-BL6, B16-F0, B16-F1, B16-F10, C1498, Colon26, CT26WT, E.G7-Ova, EL4, EMT6, H22, Hepa1-6, J558, J774A1, JC, KLN205, L1210, L5178-R, LLC, MBT2, MC38, MPC-11, Neuro-2a, P388D1, P815, Pan02, Renca, RM1, S91, and WEHI164.